3VVU | pdb_00003vvu

Crystal structure of reconstructed bacterial ancestral NDK, Bac1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.221 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3VVU

This is version 1.3 of the entry. See complete history

Literature

Experimental evidence for the thermophilicity of ancestral life

Akanuma, S.Nakajima, Y.Yokobori, S.Kimura, M.Nemoto, N.Mase, T.Miyazono, K.Tanokura, M.Yamagishi, A.

(2013) Proc Natl Acad Sci U S A 110: 11067-11072

  • DOI: https://doi.org/10.1073/pnas.1308215110
  • Primary Citation Related Structures: 
    3VVT, 3VVU

  • PubMed Abstract: 

    Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.


  • Organizational Affiliation
    • Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.

Macromolecule Content 

  • Total Structure Weight: 31.24 kDa 
  • Atom Count: 2,251 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 278 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B
139N/AMutation(s): 0 
EC: 2.7.4.6

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.349α = 90
b = 109.349β = 90
c = 109.349γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references